Download Ingenuity Variant Analysis

Index
BIOBASE REPORT ............................................................................................................................................... 2
INGENUITY VARIANT ANALYSIS .................................................................................................................. 5
DIPLOID REPORT ................................................................................................................................................. 6
GENETALK REPORT........................................................................................................................................ 22
1
BIOBASE Report
Output file format explanations for Supplementary material spreadsheet
Suppl_BIOBASEAnalysis.xlsx
HGMD Variant Type: This is the primary focus for finding interesting variants, and most
interesting are the disease-causing variants. Predisposing variants tend not to have
complete penetrance: one can easily harbour some, without having or ever getting the
disease. It means that there is some evidence from a study.
DM means the variant is flagged as having been reported to cause or contribute to
disease. ‘DM?’ means the same, but there are doubts about the report, due to other
reports, the variant being very common, or insufficient supporting evidence in the paper.
FTV are frameshift/truncating variants, DFP polymorphism associated with disease and
functionally characterised, DP polymorphism associated with disease, DF
polymorphisms functionally characterised.
HGMD Match exactness: bases means that the variant matched the known disease
causing variant, with the very same base change. Sometimes the gene and thus the
HGMD variant are reported on the negative strand, so the nucleotides listed in HGMD
may appear to be the complementary bases to the ones in the VCF file, which reports
always on the positive strand. coords means the variant just overlaps a known HGMD
mutation, but does not show the same single nucleotide base change. We only check
exact nucleotides for SNVs, any insertions/deletions are by default checked only by
coords. Base matching variants are more interesting than ones just overlapping, but one
really has to look at each case.
HGMD Disease: lists the disease or phenotype associated with the variant.
As HGMD does not record if a variant is causing disease in a dominant, recessive or
other manner, as additional context we provide:
 Zygosity: says if the subject had one or two different alleles of the variant in the
sample data.
 Inheritance: this is not specific to the variant, but is a statement about how a
disease associated to the gene of the variant may be inherited, the data are from
OrphaNet.
 Allele Frequency: this is from the CEU pilot of the 1000 Genomes project, we
also added EVS counts for comparison. If these counts are high, it would be an
indication that the variant is probably not harmful.
2
Analysis commentary
The major variants under these criteria are
1. CM060322 ALys amyloidosis, systemic in LYZ, which Son inherits also
homozygously from parents who are heterozygotes, where the allele is relatively
rare in the general population. It also is nonsynomyous coding, and predicted
deleterious by MutPred (see below).
2. CD054974, Allogenic cytotoxic T lymphocyte response in P2RX5 is a frameshift
deletion, again with parents being heterozygote, Son homozygous (see below).
3. CS042144, Altered splicing, in CFTR, the cystic fibrosis gene. Son has a
coordinate match for being homozygous for this. The variant appears because
Mother has the pathogenic allele in heterozygous fashion. In any case, this is a
disease-associated polymorphism (see below).
3
4. CM057373, Preeclampsia in STOX1. Son is homozygous, with an exact base
match, for this variant. However, Preeclampsia is a condition only relevant in
pregnancy.
These are the only DMs, for which Son is homozygous. There also is one variant, for
which Son is heterozygous, but the gene of which has been described to pass on the
disease in a dominant manner:
5. CD097476, Long QT syndrome in KCNH2. However, this is just a coordinate,
match, the pathogenic mutation is a frameshift, while Son’s is merely a SNV, and
a synonymous one at that, which is quite common in the population, in fact is the
more common allele than the one in the reference.
Son is a carrier of a variant in TCOF1, which is associated with Treacher-Collins
syndrome, some of which variants are inherited in a dominant manner. However, Son’s
allele again is relatively common, and also only matches by coordinates, so this is
probably not relevant either. For predicted genotype-phenotype associations for the
other members of the Corpas family please refer to supplementary Table 1
(Suppl_BIOBASEAnalysis.xlsx).
4
Ingenuity Variant Analysis
A series of filters used by Ingenuity variant analysis to construct a dominant
inheritance model is given in Supplementary Figure S1. Variant summary and overview
of the predictions are given in different spreadsheets of MS Excel file
(Suppl_IngenuityVariantAnalysis.xls). Annotated variants of the dataset at Genetic
analysis filter for dominant inheritance model (57 variants associated with 60 genes) are
given in Table S2. Gene models that have one or more variants and distinct disease
phenotypes associated with the variants are given in Tables S3 and S4, respectively.
An enrichment analysis p-value performed based on the number of variants of each
category is provided. The p-value refers to the significance of category. The pathways,
gene groups or complexes and, distinct molecular and cellular processes of the variants
are also given (see spreadsheet).
 Filtered variants of call quality < 20 in samples, outside top 5% most
exonically variable 100base windows in healthy public genomes, and outside top 1%
most exonically variable genes in 1000 genomes
 Excluded variants with an allele frequency of at least 3% observed in
the 1000 Genomes Project, public Complete Genomics genomes and
Exome Sequencing Project of the National Heart Lung and Blood Institute
 Retained variants that were experimentally observed to be associated with a
phenotype: pathogenic and likely pathogenic or associated with gain of function of
a gene: established in the literature or associated with loss of function of a gene:
Frameshift, in-frame indel, or start/stop codon change and missense and not
predicted tolerated by SIFT or PolyPhen-2
 Genetic analysis (GA) filter for ‘Dominant’ variants
Restricted to ‘transmitted’ variants and ‘heterozygous’ genotype in cases and,
with genotype occurrence in 2 of the 2 case samples at variant level;
Excluded genotypes except ‘heterozygous’ in controls and,
with genotype occurrence in at least 1 of the 2 control samples at variant level
 Second Genetic Analysis (GA) filter
Excluded ‘homozygous’ and ‘heterozygous’ genotypes in controls and, with
genotype occurrence in at least 2 of the 2 control samples at variant level.
Supplementary Figure S1: Filter cascade used for variant analysis on four samples Sister, Son, Father
and Mother. The series of filters used are shown: ‘Confidence’, ‘Common Variants’, ‘Predicted
Deleterious’ and ‘Genetic Analysis’ for dominant inheritance model. Under each filter the number to the
left indicates the number of variants that remain in the dataset after applying the respective filter and all
filters above it. The number on the right indicates the number of distinct genes within which those
variants are observed.
5
Diploid Report
SNPs of unconfirmed significance
SNPs for which a preliminary association with HIV-resistance and thiopurine toxicity has
been reported (but overall currently of unknown clinical relevance):
HIV resistance
All four family members might be more resistant to infection with the most common
strain of HIV (HIV-1). This is indicated by the heterozygous CT or homozygous TT calls
for Mother, Father, and Son and Daughter, respectively, for the rs3775291
polymorphism within the TLR3 gene. TLR3 contributes in the activation of antiviral
immune responses. The L412F polymorphism was recently shown to have a protective
effect against HIV infection, in a dominant fashion. However, given the limited amount of
data currently available, the impact of the rs3775291 polymorphism on HIV resistance is
still preliminary.
1. Sironi M, Biasin M, Cagliani R, Forni D, De Luca M, Saulle I, Lo Caputo S,
Mazzotta F, Macías J, Pineda JA, Caruz A, Clerici M. (2012). A common
polymorphism in TLR3 confers natural resistance to HIV-1 infection. J Immunol.,
188(2):818-23. doi: 10.4049/jimmunol.1102179.
2. Huik K, Avi R, Pauskar M, Kallas E, Jõgeda EL, Karki T, Marsh K, Des Jarlais D,
Uusküla A, Lutsar I (2013). Association between TLR3 rs3775291 and resistance
to HIV among highly exposed Caucasian intravenous drug users. Infection,
Genetics and Evolution, 20: 78–82.
Thiopurine toxicity
Father and Daughter both carry one normal and one variant copy of the TPMT gene,
denoted as TPMT*9 (rs151149760). TPMT, or thiopurine methyltransferase is an
enzyme that inactivates thiopurine drugs, which are used to treat certain cancers of the
bone marrow, various auto-immune diseases and transplant patients. Individuals with
reduced activity of the TPMT enzyme are more likely to suffer from toxic effects
following treatment with conventional doses of these drugs. The exact functional status
and pharmacogenomic implications of the extremely rare TPMT*9 allele are still
preliminary. Although TPMT*9 has been suggested to have reduced enzyme activity
and possible implications for thiopurine toxicity, the allele has both been detected in
patients with an intermediate TPMT phenotype as well as in a patient with normal TPMT
activity.
1.
Garat, A., Cauffiez, C., Renault, N., Lo-Guidice, J. M., Allorge, D., Chevalier, D.,
et al. (2008). Characterisation of novel defective thiopurine S-methyltransferase allelic
variants. Biochemical pharmacology, 76(3), 404–415. doi:10.1016/j.bcp.2008.05.009
6
2.
Relling, M. V., Gardner, E. E., Sandborn, W. J., Schmiegelow, K., Pui, C.-H.,
Yee, S. W., et al. (2011). Clinical Pharmacogenetics Implementation Consortium
Guidelines for Thiopurine Methyltransferase Genotype and Thiopurine Dosing. Clinical
Pharmacology & Therapeutics, 89(3), 387–391. doi:10.1038/clpt.2010.320
3.
Ujiie, S., Sasaki, T., Mizugaki, M., Ishikawa, M., & Hiratsuka, M. (2008).
Functional characterization of 23 allelic variants of thiopurine S-methyltransferase gene
(TPMT*2 – *24). Pharmacogenetics and Genomics, 18(10), 887–893.
doi:10.1097/FPC.0b013e3283097328
PRSS1-related hereditary pancreatitis
Although we cannot draw conclusions from the variants identified in this analysis, we
were intrigued when finding several variants within the PRSS1 gene for all four family
members.
The standard Diploid analysis identified rs111033566 within PRRS1 as heterozygous
for all four family members, a SNP which has been repeatedly reported as being
pathogenic for PRSS1-related Hereditary Pancreatitis. As mentioned in the previous
report, we assumed incomplete penetrance contributed to the fact that none of the
family members were affected. However, the results from the extended analysis of the
exome data now raise some doubt about the reliability of the heterozygous call for
rs111033566, as well as the other calls in PRSS1.
In addition to rs111033566, all four family members have heterozygous calls for some
other, positions within the PRSS1 gene (currently of unknown significance). Although
the coverage depth is high for all calls (as it was for rs111033566), there is an
imbalance in allelic depth. For heterozygous calls, we would expect an equal amount of
sequences containing the reference or alternative allele (giving an 1:1 ratio). However,
for all heterozygous calls within PRSS1, this ratio deviates from the expected 1:1 ratio.
PRSS1
SNP/position
Family member
Genotype
Allelic depth
(Ref/Alt)
rs111033566
Father
Heterozygous GA
56/37
Mother
Heterozygous GA
58/32
Daughter
Heterozygous GA
64/31
Son
Heterozygous GA
76/60
Father
Heterozygous GA
63/21
Mother
Heterozygous GA
55/31
Daughter
Heterozygous GA
66/30
Son
Heterozygous GA
140/28
142459679
7
PRSS1
SNP/position
Family member
Genotype
Allelic depth
(Ref/Alt)
142460339
Father
Heterozygous GA
147/15
Mother
Heterozygous GA
132/27
Daughter
Heterozygous GA
135/42
Son
Homozygous Ref.
-
Father
Heterozygous GA
69/49
Mother
Heterozygous GA
71/36
Daughter
Heterozygous GA
69/49
Son
Heterozygous GA
105/52
Father
Heterozygous TC
65/25
Mother
Heterozygous TC
68/15
Daughter
Heterozygous TC
77/17
Son
Heterozygous TC
103/22
142460369
142460394
We therefore had another look at the data. In particular, we looked at the accuracy of
the calls predicted by the Variant Quality Score Recalibration, which gives a single
estimate for the accuracy of each call by comparing the VQSLOD scores of each variant
with a calculated threshold value (for detailed info on this parameter, see
http://gatkforums.broadinstitute.org/discussion/39/variant-quality-score-recalibrationvqsr). Variants that are above the threshold are considered of good accuracy (‘PASS’ in
filter column), variants for which VQSLOD falls below the threshold, are considered
false positives.
In the vcf-files, there is only information about this filtering step for one of the samples.
However, all variants within PRSS1 (also rs111033566 that came out of the standard
analysis) seem to be false positive calls, based on this threshold. Although it is not clear
why the PRSS1 calls all turn out to be false positive.
In conclusion, the positive result for Hereditary pancreatitis is probably due to a false
positive call for rs111033566.
Comments and details for the other rare variants are given below. Variants that seem to
be accurately called are indicated in orange, however, the variants remain of unknown
clinical significance.
SON
8
Red (Polyphen and Sift scores above the threshold)
1.
DYSF (only found in Son): CT heterozygous: potentially related to a carrier status
of autosomal recessive limb girdle muscular dystrophy 2B or Miyoshi myopathy,
Sequencing depth 17 ok, imbalance in allele depth (13:4), PASS, GQ ok (99), Phred
likelihood (102, 0, 409); based on the imbalance in allele depth, the alternative base
call might be inaccurate.
2.
SLC25A20 (only found in Son): CA heterozygous: potentially related to a carrier
status of carnitine-acylcarnitine translocase deficiency, a metabolic disorder. allele
depth (1:2), low sequencing depth (3), low GQ (27), PASS, PL (66, 0, 27), based on
GQ and sequencing depth probably an inaccurate call.
3.
HNF1A (idem Mother): GA heterozygous: potentially pathogenic for MODY3
(dominant), low sequencing depth (4), low allele depth (1:3), low GQ, PASS, PL (107, 0,
17), based on GQ and low sequencing depth probably an inaccurate call.
4.
LAMA3 (idem Daughter and Mother): CA heterozygous: potentially related to a
carrier status of epidermolysis bullosa, a skin disorder (ranges from mild to severe),
sequencing depth (23) seems ok, allele depth (13,10) ok, GQ 99 ok, PASS, PL (294, 0,
425), seems to be an accurate call, however the variant itself remains of unknown
clinical significance.
5.
RHPN2 (idem Daughter and Father): TC heterozygous: this gene has not yet
been shown to be associated with a genetic disease or trait, its protein product plays a
role in the organisation of the actin cytoskeleton. sequencing depth (69) ok, allele depth
(43, 26) imbalance?, GQ 99 ok, PL (440, 0, 778), VQSRTrancheSNP99.90to100.00
(though not clear whether this applies to the sample of the Son), based on VQSR and
allele imbalance probably a false positive call.
Orange (Sift or Polyphen score above the threshold):
1.
HSPD1 (idem Daughter and Mother): CT heterozygous: potentially related to a
carrier status of autosomal recessive spastic paraplegia 13, polyphen 0,85, sequencing
depth (41) ok, allele depth (32:9) imbalance?, GQ 99 ok, PL (174, 0, 1112),
VQSRTrancheSNP99.00to99.90, based on VQSR and allele imbalance probably a
false positive call.
2.
ARX (idem Mother?; in vcf Mother genotype ./. is indicated): TT homozygous alt:
potentially pathogenic for X-linked mental retardation and epilepsy. Sift 0,03, low
sequencing depth (2), allele depth (0:2), low GQ (6), PL (78, 6, 0), PASS (! in vcf
genotype: 1/1, this gene is located on the X-chormosome, call needs to be haploid for
the son, thus carries the alt allele T according to the vcf), based on low sequencing
depth and low GQ probably an inaccurate call.
Grey:
did not pass the Sift and/or Polyphen thresholds + no reliable homozygous calls
White (no Sift and/or Polyphen scores available):
1.
CLCNKA (only found in Son): TC heterozygous: potentially related to a carrier
status of Bartter syndrome with sensorineural deafness, a kidney disorder combined
with sensorineural deafness, sequencing depth (34) ok, allele depth (27:7) imbalance,
low GQ (71), PL (71, 0, 637), VQSRTrancheSNP99.90to100.00, based on VQSR and
allele imbalance probably a false positive call.
9
2.
PYHIN1 (idem Daughter and Father): CT heterozygous: this gene has not yet
clearly been correlated to a certain disease or trait, it functions as a tumor suppressor,
in that respect down regulation of this gene is associated with breast cancer,
sequencing depth: 11 rather low, allele depth (4:7) imbalance, GQ 99 ok, PL (235, 0,
123), PASS, based on imbalance in allele depth probably an inaccurate call,
though GQ and VQSR seem ok.
3.
FCGR2B (idem Daughter & Father, both very low GQ): TG heterozygous: this
gene has not yet clearly been correlated to a certain disease or trait, it is involved in
phagocytosis of immune complexed and antigen production regulation, variations might
increase susceptibility to systemic lupus erythematosus. Sequencing depth (19) ok,
allele depth (14, 5) imbalance, GQ 12 low, PL (12, 0, 140),
VQSRTrancheSNP99.90to100.00, Based on VQSR, allele imbalance and low GQ
probably a false positive call.
4.
PKP1 (idem Daughter & Mother, both very low GQ): GT heterozygous: potentially
related to a carrier status of ectodermal dysplasia - skin fragility syndrome, a skin
disorder. sequencing depth (2) low, allele depth (1:1), low GQ (32), PL (32, 0, 34),
PASS, Based on the low sequencing depth and low GQ probably an inaccurate
call.
5.
ALMS1 (idem Father): AG heterozygous: potentially related to a carrier status of
Alström syndrome, a multi systemic disorder, characterised by childhood obesity,
blindness, hearing loss and other symptoms. polyphen (0,985), sequencing depth (18)
+/- ok, allele depth (11, 7) ok, GQ 99 ok, PL (222,0,367), PASS, Seems to be an
accurate call, however, the variant itself remains of unknown clinical significance.
6.
ZAP70 (only found in Son): CA heterozygous: potentially related to a carrier
status of ZAP70-related severe combined immunodeficiency, an immune disorder.
Sequencing depth (24) ok, allele depth (20, 4) imbalance, GQ (81) rather low, PL (81, 0,
677), polyphen 0,988, VQSRTrancheSNP99.00to99.90, Based on VQSR and allele
imbalance probably a false positive call.
7.
HS6ST1 (idem Daughter & Mother, but both low GQ): GA heterozygous: This
gene has not yet been associated with a certain disease or trait, it functions as an
enzyme involved in generating heparin sulcate fine structures. Sequencing depth (60)
ok, allele depth (49,11) imbalance, low GQ (5), PL (5, 0, 558),
VQSRTrancheSNP99.90to100.00, Based on allele imbalance, VQSR and low GQ
probably a false positive call.
8.
HS6ST1 (idem Mother & Father, but both low GQ): GT heterozygous: see
previous one, sequencing depth (28) ok, allele depth (12,16) ok, GQ 99 ok, PL (207, 0,
102), VQSRTrancheSNP99.90to100.00, Based on VQSR probably a false positive
call.
9.
… (low GQ, VQSR, low depth, allele imbalance, no genotype (./.) …)
10.
SMARCAL1 (idem Daughter and Father): CT heterozygous, potentially related to
a carrier status of Schimke immuno-osseous dysplasia, characterised by short stature,
kidney disease and a weakened immune system. Sequencing depth (54) ok, allele
depth (29, 25) ok, GQ (99) ok, PL (785, 0, 892), PASS, seems to be an accurate call,
however the variant itself remains of unknown clinical significance + unknown
Sift and polyphen scores.
10
11.
MANBA (idem Daughter & Father, but in both samples no genotype call): TT
homozygous: potentially pathogenic for beta-mannosidosis, a lysososmal storage
disease with neurological involvement. sequencing depth (2) low, allele depth (0,2) low,
(! genotype in vcf: 1/1???), GQ (6) low, PL (79,6,0), PASS, Based on low sequencing
depth and GQ probably an inaccurate call.
12.
LAMA2 (idem Daughter & Mother): CT heterozygous: potentially related to a
carrier status of congenital merosin-deficient muscular dystrophy. Sequencing depth: 49
ok, allele depth (28;21) ok, GQ: 99, PL (643, 0, 907), PASS, seems to be an accurate
call, however the variant itself remains of unknown clinical significance +
unknown Sift and polyphen scores.
13.
SYNE1 (idem Father): GCTTG heterozygous: potentially related to a carrier
status of autosomal recessive cerebellar ataxia type 1. Sequencing depth (64) ok, allele
depth (33,30), GQ 99 ok, PL (1451, 0, 1264), PASS, seems to be an accurate call,
however the variant itself remains of unknown clinical significance + unknown
Sift and polyphen scores.
14.
CNTNAP2 (idem Daughter & Mother, low GQ in sample daughter): TC
heterozygous: this gene has not yet been correlated to a certain disease or trait, it plays
a role as cell adhesion molecules and receptors in neurons, it has been implicated in
some neurodevelopmental disorders such as Gilles de la Tourette syndrome,
schizophrenia, epilepsy, autism, ADHD, and mental retardation. Sequencing depth (41)
ok, allele depth (31,10) imbalance, GQ 99, pL (242,0,910), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical significance
+ unknown Sift and polyphen scores.
15.
DPYS (idem Daughter & Mother): AG heterozygous: potentially related to a
carrier status of dihydropyriminidase deficiency, ranges from asymptomatic to
neurological problems. Sequencing depth (33) ok, allele depth (20,13) imbalance?, GQ
99 ok, PL (392,0,651), PASS, seems to be an accurate call, however the variant
itself remains of unknown clinical significance + unknown Sift and polyphen
scores.
16.
HOGA1 (idem Daughter & Father) : CT heterozygous: potentially related to a
carrier status of primary hyperoxaluria type 3, which can cause kidney damage.
sequencing depth (61) ok, allele depth (24,37) imbalance?, GQ99 ok, PL (973,0,788),
PASS, seems to be an accurate call, however the variant itself remains of
unknown clinical significance + unknown Sift and polyphen scores.
17.
SLCO1B3 (idem Father): TA heterozygous: this gene has been associated with
Rotor type hyperbilirubinemia, it functions as a transporter in the liver and plays a role in
bile acid and bilirubin transport. Sequencing depth (59) ok, allele depth (44,15)
imbalance, GQ 99 ok, PL (413,0,1479), PASS, Polyphen score 1, seems to be an
accurate call, however the variant itself remains of unknown clinical significance
+ allele imbalance?.
18.
EIF2B2 (idem Daughter & Father): AG heterozygous: potentially related to a
carrier status of leukoencephalopathy with vanishing white matter, a progressive
neurological disorder. Sequencing depth (86) ok, allele depth (55,31) imbalance, GQ 99
ok, PL (940, 0, 1812), Polyphen score 0,948, seems to be an accurate call, however
the variant itself remains of unknown clinical significance + allele imbalance.
11
19.
IFT140 (idem Daughter & Mother): CT heterozygous: this gene has not yet been
correlated to a certain disease or trait, plays a role in cilia function (potential role in
kidney function). Sequencing depth (50) ok, allele depth (30,20) ok, GQ 99 ok, PL
(618,0,869), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen scores.
20.
DNM2 (idem Father): CT heterozygous: potentially pathogenic for centronuclear
myopathy, that affects skeletal muscles, or Charcot-Marie Tooth disease, a neurological
disorder with progressive muscle weakness. sequencing depth (27) ok, allele depth
(13,14) ok, GQ 99 ok, PL (371,0,308), PASS, seems to be an accurate call, however
the variant itself remains of unknown clinical significance + unknown Sift and
polyphen scores.
21.
COL6A2 (idem Daughter & Father, daughter low GQ and depth): AAC
heterozygous: potentially pathogenic for Bethlem myopathy or related to a carrier status
of Ullrich congenital muscular dystrophy, sequencing depth: 47 ok, allele depth (25,21)
ok, GQ 99 ok, PL (823,0,634), PASS, seems to be an accurate call, however the
variant itself remains of unknown clinical significance + unknown Sift and
polyphen scores.
22.
XPNPEP3 (idem Daughter & Father): TTA heterozygous: potentially related to a
carrier status of nephronophthisis-like nephropathy, a kidney disease. Sequencing
depth (78) ok, allele depth (47, 30), imbalance?, GQ 99 ok, PL 1229,0,1829, PASS,
seems to be an accurate call, however the variant itself remains of unknown
clinical significance + unknown Sift and polyphen scores.
DAUGHTER
Red (Polyphen and Sift scores above the threshold):
1.
CACNA1S (only found in Daughter): GA heterozygous: potentially pathogenic for
hypokalemic periodic paralysis and/or malignant hyperthermia susceptibility.
Sequencing depth: 3 low, allele depth (1,2) low, GQ: 31, PL (69,0,31), PASS, Based on
low sequencing depth and GQ probably an inaccurate call.
2.
WDPCP (idem Mother): AT heterozygous: potentially related to a carrier status of
Meckel-Gruber syndrome, and/or Bardet-Biedl syndrome, two developmental disorders.
Sequencing depth 22 ok, allele depth (9,13) ok, GQ 99 ok, PL (421,0,280), PASS,
seems to be an accurate call, however the variant itself remains of unknown
clinical significance.
3.
SERPINI1 (idem Father): GA heterozygous: potentially pathogenic for familial
encephalopathy with neuroserpin inclusion bodies, a progressive neurodegenerative
disorder. Sequencing depth 38 ok, allele depth (25,13) imbalance?, GQ 99 ok, PL (371,
0,853), VQSRTrancheSNP99.00to99.90, Based on VQSR and allele depth probably
a false positive call.
4.
CCHCR1 (idem Father): GC heterozygous: this gene has not yet been
associated with a certain disease or trait (except preliminary nevirapine hypersensitivity
and psoriasis susceptibility), it encodes coiled-coil alpha helical rod protein 1.
Sequencing depth: 26 ok, allele depth (12,14) ok, GQ 99 ok, PL (375,0,363), PASS,
12
seems to be an accurate call, however the variant itself remains of unknown
clinical significance.
5.
LAMA3 (idem Son & Mother): CA heterozygous: potentially related to a carrier
status of epidermolysis bullosa, a skin disorder (ranges from mild to severe),
sequencing depth (21) seems ok, allele depth (15,6) imbalance, GQ 99 ok, PASS, PL
(162, 0, 533), seems to be an accurate call, however the variant itself remains of
unknown clinical significance.
6.
RHPN2 (idem Son & Father): TC heterozygous: this gene has not yet been
shown to be associated with a genetic disease or trait, its protein product plays a role in
the organisation of the actin cytoskeleton. sequencing depth (29) ok, allele depth (20, 9)
imbalance, GQ 56 low, PL (56, 0, 476), VQSRTrancheSNP99.90to100.00, based on
VQSR, low GQ and allele imbalance probably a false positive call.
Orange (Sift or Polyphen score above the threshold):
1.
HSPD1 (idem Son & Mother): CT heterozygous: potentially related to a carrier
status of autosomal recessive spastic paraplegia 13, polyphen 0,85, sequencing depth
(50) ok, allele depth (44:6) imbalance, GQ 74 low, PL (74, 0, 1582),
VQSRTrancheSNP99.00to99.90, based on VQSR, low GQ and allele imbalance
probably a false positive call.
2.
ABCC3 (idem Mother, but low GQ): AC heterozygous: This gene has not yet
been associated to a certain disease or trait, functions as a transporter, potentially
involved in multidrug resistance, Sequencing depth: 9 low, allele depth: 8:1, low, GQ 16
low, PL (16,0,219), PASS, Based on low sequencing depth, GQ and allele
imbalance, probably an inaccurate call.
3.
CD177 (idem Mother): GC heterozygous: this gene has not yet been associated
to a certain disease or trait, encodes a cell surface glycoprotein, was first described in a
case of neonatal alloimmune neutropenia. Sequencing depth (18) ok, allele depth (9:9)
ok, GQ 99 ok, PL (253,0,273), PASS, seems to be an accurate call, however the
variant itself remains of unknown significance.
4.
NLRP12 (idem Mother): CG heterozygous: potentially pathogenic for familial cold
auto inflammatory syndrome, which causes episodes of fever, skin rash and joint pain
after exposure to cold temperatures. Sequencing depth (19) ok, allele depth (11,8) ok,
GQ 99 ok, PL (225,0,363), PASS, seems to be an accurate call, however the variant
itself remains of unknown significance.
Grey:
did not pass the Sift and/or Polyphen thresholds + no reliable homozygous calls
White (no Sift and/or Polyphen scores available): suspicious:
1.
PYHIN1 (idem Son & Father): CT heterozygous: this gene has not yet clearly
been correlated to a certain disease or trait, it functions as a tumor suppressor, in that
respect down regulation of this gene is associated with breast cancer, sequencing
depth: 28 ok, allele depth (19:9) imbalance, GQ 99 ok, PL (264, 0, 672), PASS, based
on imbalance in allele depth probably an inaccurate call, though GQ and VQSR
seem ok.
13
2.
NEB (idem Mother): GA heterozygous: potentially related to a carrier status of
nemaline myopathy, characterised by muscle weakness, scoliosis and joint deformities.
Sequencing depth (53) ok, allele depth (31, 22) imbalance?, GQ 99, PL (631,0,1066),
PASS, seems to be an accurate call, however the variant itself remains of
unknown clinical significance + unknown Sift and polyphen scores.
3.
SMARCAL1 (Idem Son & Father): CT heterozygous, potentially related to a
carrier status of Schimke immuno-osseous dysplasia, characterised by short stature,
kidney disease and a weakened immune system. Sequencing depth (42) ok, allele
depth (23, 19) ok, GQ (99) ok, PL (541, 0, 782), PASS, seems to be an accurate call,
however the variant itself remains of unknown clinical significance + unknown
Sift and polyphen scores.
4.
CUL7 (Idem Father): CG heterozygous, potentially related to a carrier status of 3M syndrome type 1, a cause of dwarfism. Sequencing depth (17) ok, allele depth (8,9)
ok, GQ 99 ok, PL (272, 0, 255), PASS, seems to be an accurate call, however the
variant itself remains of unknown clinical significance + unknown Sift and
polyphen scores.
5.
RIMS1 (idem Father): GA heterozygous, potentially pathogenic for cone-rod
dystrophy, autosomal dominant, a hereditary eye condition. Sequencing depth (29) ok,
allele depth (12,17) ok, GQ 99 ok, PL (529,0,360), PASS, seems to be an accurate
call, however the variant itself remains of unknown clinical significance +
unknown Sift and polyphen scores.
6.
LAMA2 (idem Son & Mother): CT heterozygous: potentially related to a carrier
status of congenital merosin-deficient muscular dystrophy. Sequencing depth: 38 ok,
allele depth (25;13) imbalance?, GQ: 99, PL (404, 0, 881), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical significance
+ unknown Sift and polyphen scores.
7.
DPYS (idem Son & Mother): AG heterozygous: potentially related to a carrier
status of dihydropyriminidase deficiency, ranges from asymptomatic to neurological
problems. Sequencing depth (34) ok, allele depth (21,13) imbalance?, GQ 99 ok, PL
(389,0,718), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen scores.
8.
HOGA1 (idem Son & Father): CT heterozygous: potentially related to a carrier
status of primary hyperoxaluria type 3, which can cause kidney damage. sequencing
depth (19) ok, allele depth (14,5) imbalance?, GQ99 ok, PL (133,0,486), PASS, seems
to be an accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
9.
WNK1 (idem Mother): TC heterozygous: potentially related to a carrier status of
hereditary sensory and autonomic neuropathy type 2, impairment of pain sensations,
and/or pseudohypoaldosteronism type 2. Sequencing depth (39) ok, allele depth (21,18)
ok, GQ 99 ok, PL (581,0,653), PASS, seems to be an accurate call, however the
variant itself remains of unknown clinical significance + unknown Sift and
polyphen scores.
10.
FGD4 (idem Mother): CT heterozygous: potentially related to a carrier status of
Charcot-Marie-Tooth disease type 4H, a neurodegenerative disorder. Sequencing depth
(35) ok, allele depth (20,15) ok, GQ 99 ok, PL (427, 0, 590), PASS, seems to be an
14
accurate call, however the variant itself remains of unknown clinical significance
+ unknown Sift and polyphen scores.
11.
EIF2B2 (idem Son & Father): AG heterozygous: potentially related to a carrier
status of leukoencephalopathy with vanishing white matter, a progressive neurological
disorder. Sequencing depth (76) ok, allele depth (42,34) imbalance?, GQ 99 ok, PL
(1114, 0, 1417), Polyphen score 0,948, PASS seems to be an accurate call, however
the variant itself remains of unknown clinical significance + allele imbalance?
12.
PIF1 (idem Father): AC heterozygous: This gene has not yet been associated
with a certain disease or trait, it functions as a DNA helicase that negatively regulates
telomerase, a reverse transcriptase that maintains telomere length. Sequencing depth
(9) rather low, allele depth (4,5) ok, GQ 99, PL (154,0,131), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical significance
+ unknown Sift and polyphen scores.
13.
IFT140 (idem Son & Mother): CT heterozygous: this gene has not yet been
correlated to a certain disease or trait, plays a role in cilia function (potential role in
kidney function). Sequencing depth (12) ok, allele depth (7,5) ok, GQ 99 ok, PL
(153,0,215), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen scores.
14.
HNF1B (idem Father): GT heterozygous: potentially pathogenic for MODY5
and/or renal cysts. Sequencing depth: 14 ok, allele depth (8;6) ok, GQ 99 ok, PL
(196,0,257), PASS, Sift 0,05, seems to be an accurate call, however the variant
itself remains of unknown clinical significance + unknown polyphen scores.
15.
XPNPEP3 (idem Son & Father): TTA heterozygous: potentially related to a
carrier status of nephronophthisis-like nephropathy, a kidney disease. Sequencing
depth (74) ok, allele depth (36, 38), ok, GQ 99 ok, PL 1672,0,1414, PASS, seems to be
an accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
16.
SHROOM4 (idem Father): CT heterozygous: potentially related to a carrier status
of X-linked mental retardation. Sequencing depth (57) ok, allele depth (26,31) ok, GQ
99 ok, PL (1023,0,839), PASS, seems to be an accurate call, however the variant
itself remains of unknown clinical significance + unknown Sift and polyphen
scores.
MOTHER
Red (Polyphen and Sift scores above the threshold):
1.
WDPCP (idem daughter): AT heterozygous: potentially related to a carrier status
of Meckel-Gruber syndrome, and/or Bardet-Biedl syndrome, two developmental
disorders. Sequencing depth 28 ok, allele depth (18,10) ok, GQ 99 ok, PL (296,0,608),
PASS, seems to be an accurate call, however the variant itself remains of
unknown clinical significance.
2.
AGGF1 (only found in Mother): GG homozygous: potentially pathogenic for
Klippel-Trenaunay syndrome. Sequencing depth 4 low, allele depth (0:4), GQ 12 low,
PL (145,12,0), PASS, based on low sequencing depth and GQ probably an
inaccurate call.
15
3.
SYNE1 (only found in Mother): GA heterozygous : potentially related to a carrier
status of autosomal recessive spinocerebellar ataxia 8. Sequencing depth 11 rather low,
allele depth (5,6) ok, GQ 99 ok, PL (183,0,138), PASS, seems to be an accurate call,
however the variant itself remains of unknown clinical significance.
4.
LRRC14 (only found in Mother): GA heterozygous: this gene has not yet been
associated to a certain disease or trait, it encodes a leucine-rich containing protein.
Sequencing depth 16 ok, allele depth (8;7) ok, GQ 99, PL (233,0,180), PASS, seems to
be an accurate call, however the variant itself remains of unknown clinical
significance.
5.
HNF1A (idem Son): GA heterozygous: potentially pathogenic for MODY3
(dominant), low sequencing depth (4), low allele depth (2:2), low GQ 61, PASS, PL (66,
0, 61), based on GQ and low sequencing depth: inaccurate call.
6.
LAMA3 (idem Son and Daughter): CA heterozygous: potentially related to a
carrier status of epidermolysis bullosa, a skin disorder (ranges from mild to severe),
sequencing depth (39) seems ok, allele depth (17,22) ok, GQ 99 ok, PASS, PL (672, 0,
529), seems to be an accurate call, however the variant itself remains of unknown
clinical significance.
7.
DLL3 (only found in Mother): TT homozygous: potentially pathogenic for
spondylocostal dysostosis, characterised by abnormal development of the spine and
ribs. Sequencing depth: 2 low, allele depth (0,2) low, GQ 6 low, PL (73,6,0), PASS,
Based on low GQ and sequencing depth probably an inaccurate call.
8.
TAZ (only found in Mother): TT homozygous: potentially pathogenic for 3Methylglutaconic aciduria type 2, or Barth syndrome, characterized by an enlarged and
weakened heart, recurrent infections, muscle weakness and delayed growth.
Sequencing depth 2 low, allele depth (0,2) low, GQ 6 low, PL (70,6,0), PASS, Based on
low GQ and sequencing depth probably an inaccurate call.
Orange (Sift or Polyphen score above the threshold):
1.
HSPD1 (idem Son and Daughter): CT heterozygous: potentially related to a
carrier status of autosomal recessive spastic paraplegia 13, polyphen 0,85, sequencing
depth (40) ok, allele depth (33:7) imbalance, GQ 99 ok, PL (130, 0, 1114),
VQSRTrancheSNP99.00to99.90, based on VQSR and allele imbalance probably a
false positive call.
2.
ABCC3 (idem Daughter): AC heterozygous: This gene has not yet been
associated to a certain disease or trait, functions as a transporter, potentially involved in
multidrug resistance, Sequencing depth: 8 low, allele depth: 4:4, low, GQ 75 low, PL
(75,0,120), PASS, Based on low sequencing depth and GQ, probably an
inaccurate call.
3.
CD177 (idem daughter): GC heterozygous: this gene has not yet been
associated to a certain disease or trait, encodes a cell surface glycoprotein, was first
described in a case of neonatal alloimmune neutropenia. Sequencing depth (14) ok,
allele depth (6:8) ok, GQ 99 ok, PL (240,0,187), PASS, seems to be an accurate call,
however the variant itself remains of unknown significance.
4.
NLRP12 (idem daughter): CG heterozygous: potentially pathogenic for familial
cold auto inflammatory syndrome, which causes episodes of fever, skin rash and joint
pain after exposure to cold temperatures. Sequencing depth (11) rather low, allele depth
16
(8,3) imbalance?, GQ 87 low ok, PL (87,0,283), PASS, seems to be an accurate call,
however the variant itself remains of unknown significance.
Grey:
did not pass the Sift and/or Polyphen thresholds + no reliable homozygous calls
White (no Sift and/or Polyphen scores available): suspicious:
1.
NEB (idem Daughter): GA heterozygous: potentially related to a carrier status of
nemaline myopathy, characterised by muscle weakness, scoliosis and joint deformities.
Sequencing depth (51) ok, allele depth (25, 26) ok, GQ 99, PL (756,0,793), PASS,
seems to be an accurate call, however the variant itself remains of unknown
clinical significance + unknown Sift and polyphen scores.
2.
LAMA2 (idem Son and Daughter): CT heterozygous: potentially related to a
carrier status of congenital merosin-deficient muscular dystrophy. Sequencing depth: 36
ok, allele depth (22;14) imbalance?, GQ: 99, PL (442, 0, 757), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical significance
+ unknown Sift and polyphen scores.
3.
CNTNAP2 (idem Son (& daugher, low GQ)): TC heterozygous: this gene has not
yet been correlated to a certain disease or trait, it plays a role as cell adhesion
molecules and receptors in neurons, it has been implicated in some
neurodevelopmental disorders such as Gilles de la Tourette syndrome, schizophrenia,
epilepsy, autism, ADHD, and mental retardation. Sequencing depth (16) ok, allele depth
(9,7) ok, GQ 99, pL (205,0,292, PASS, seems to be an accurate call, however the
variant itself remains of unknown clinical significance + unknown Sift and
polyphen scores.
4.
DPYS (idem Son and Daughter): AG heterozygous: potentially related to a carrier
status of dihydropyriminidase deficiency, ranges from asymptomatic to neurological
problems. Sequencing depth (31) ok, allele depth (12,19) imbalance?, GQ 99 ok, PL
(601,0,371), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen scores.
5.
WNK1 (idem Daughter): TC heterozygous: potentially related to a carrier status
of hereditary sensory and autonomic neuropathy type 2, impairment of pain sensations,
and/or pseudohypoaldosteronism type 2. Sequencing depth (29) ok, allele depth (19,10)
imbalance?, GQ 99 ok, PL (246,0,557), PASS, seems to be an accurate call,
however the variant itself remains of unknown clinical significance + unknown
Sift and polyphen scores.
6.
FGD4 (idem daughter): CT heterozygous: potentially related to a carrier status of
Charcot-Marie-Tooth disease type 4H, a neurodegenerative disorder. Sequencing depth
(44) ok, allele depth (24,20) ok, GQ 99 ok, PL (603, 0, 611), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical significance
+ unknown Sift and polyphen scores.
7.
b (only found in Mother): AT heterozygous: potentially pathogenic for familial
breast and ovarian cancer. Sequencing depth 39 ok, allele depth (15,24) imbalance?;
GQ 99 ok, PL (737,0,443), PASS, seems to be an accurate call, however the variant
itself remains of unknown clinical significance + unknown Sift and polyphen
scores.
17
8.
SYNE2 (only found in Mother): GA heterozygous: this gene has not yet been
associated with a certain disease or trait, the encoded protein maintains the structural
integrity of the nucleus. Sequencing depth 17 ok, allele depth (11,6) imbalance?; GQ 99
ok, PL (187,0,379), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen scores.
9.
IFT140 (idem Son and daughter): CT heterozygous: this gene has not yet been
correlated to a certain disease or trait, plays a role in cilia function (potential role in
kidney function). Sequencing depth (17) ok, allele depth (12,5) imbalance?, GQ 99 ok,
PL (139,0,336), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen scores.
10.
MAP3K15 (only found in Mother): GA heterozygous: this gene has not yet been
associated with a certain disease or trait, it plays a role in apoptotic cell death triggered
by cellular stresses. Sequencing depth (64) ok, allele depth (37,27) ok, GQ 99 ok, PL
(831, 0,1224), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen scores.
FATHER
Red (Polyphen and Sift scores above the threshold):
1.
SERPINI1 (idem daughter): GA heterozygous: potentially pathogenic for familial
encephalopathy with neuroserpin inclusion bodies, a progressive neurodegenerative
disorder. Sequencing depth 43 ok, allele depth (23,20) ok, GQ 99 ok, PL (578, 0,732),
VQSRTrancheSNP99.00to99.90, Based on VQSR probably a false positive call.
2.
CCHCR1 (idem Daughter): GC heterozygous: this gene has not yet been
associated with a certain disease or trait (except preliminary nevirapine hypersensitivity
and psoriasis susceptibility), it encodes coiled-coil alpha helical rod protein 1.
Sequencing depth: 32 ok, allele depth (15,17) ok, GQ 99 ok, PL (445,0,467), PASS,
seems to be an accurate call, however the variant itself remains of unknown
clinical significance.
3.
ERCC6 (only found in Father): CG heterozygous: potentially related to a carrier
status of Cerebrooculofacioskeletal syndrome, Cockayne syndrome, and/or UVsensitive syndrome, disorders that affect bone and joint development and are
characterized by extreme sensitivity to sunlight. Sequencing depth: 22 ok, allele depth
(11:11) ok, GQ 99 ok, PL (364,0,359), PASS, seems to be an accurate call, however
the variant itself remains of unknown clinical significance.
4.
RHPN2 (idem Son and Daughter): TC heterozygous: this gene has not yet been
shown to be associated with a genetic disease or trait, its protein product plays a role in
the organisation of the actin cytoskeleton. sequencing depth (28) ok, allele depth (16,
12) ok, GQ 99 ok, PL (188, 0,220), VQSRTrancheSNP99.90to100.00, based on VQSR,
low GQ and allele imbalance probably a false positive call.
Orange (Sift or Polyphen score above the threshold):
1.
XDH (only found in Father): CA heterozygous: potentially related to a carrier
status of Xanthinuria type 1, a metabolic disorder. Sequencing depth: 19 ok, allele depth
18
(15,4) imbalance?, GQ 79 low, PL (79,0,536), PASS, Based on low GQ and allele
imbalance probably an inaccurate call.
2.
LAMA2 (only found in Father): AG heterozygous: potentially related to a carrier
status of congenital merosin-deficient muscular dystrophy. Sequencing depth: 27 ok,
allele depth (14;13) ok, GQ: 99, PL (438, 0,449), PASS, Sift 0,01; seems to be an
accurate call, however the variant itself remains of unknown clinical significance.
3.
SEC23B (only found in Father): GA heterozygous: potentially related to a carrier
status of congenital dyserythropoietic anemia type 2, an inherited blood disorder.
Sequencing depth 39 ok, allele depth (20,19) ok, GQ 99, PL (612,0,634), PASS; seems
to be an accurate call, however the variant itself remains of unknown clinical
significance.
Grey:
did not pass the Sift and/or Polyphen thresholds + no reliable homozygous calls
White (no Sift and/or Polyphen scores available): suspicious:
1. PYHIN1 (idem Son and Daughter): CT heterozygous: this gene has not yet
clearly been correlated to a certain disease or trait, it functions as a tumor
suppressor, in that respect down regulation of this gene is associated with
breast cancer, sequencing depth: 22 ok, allele depth (15:7) imbalance, GQ 99
ok, PL (207, 0, 530), PASS, based on imbalance in allele depth probably an
inaccurate call, though GQ and VQSR seem ok.
2. ALMS1 (idem Son): AG heterozygous: potentially related to a carrier status of
Alström syndrome, a multi systemic disorder, characterised by childhood
obesity, blindness, hearing loss and other symptoms. polyphen (0,985),
sequencing depth (31) ok, allele depth (15,16) ok, GQ 99 ok, PL (539,0,459),
PASS, Seems to be an accurate call, however, the variant itself remains of
unknown clinical significance + unknown Sift score.
3. SMARCAL1 (idem Son & Daughter): CT heterozygous, potentially related to a
carrier status of Schimke immuno-osseous dysplasia, characterised by short
stature, kidney disease and a weakened immune system. Sequencing depth
(25) ok, allele depth (12, 13) ok, GQ (99) ok, PL (397, 0,353), PASS, seems to
be an accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
4. MSH3 (only found in Father): AG heterozygous: this gene has not yet clearly
been associated with a certain disease or trait, functions in the post-replicative
DNA mismatch repair system. Defects in this gene may confer susceptibility to
endometrial cancer. Sequencing depth: 19 ok, allele depth: 9;10 ok, GQ 99 ok,
PL (342,0,291), PASS, Polyphen: 0,971, seems to be an accurate call,
however the variant itself remains of unknown clinical significance +
unknown Sift score.
5. CUL7 (idem Daughter): CG heterozygous, potentially related to a carrier status
of 3-M syndrome type 1, a cause of dwarfism. Sequencing depth (12) rather
low, allele depth (6,6) ok, GQ 99 ok, PL (193, 0,195), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
19
6. RIMS1 (idem Daughter): GA heterozygous, potentially pathogenic for cone-rod
dystrophy, autosomal dominant, a hereditary eye condition. Sequencing depth
(28) ok, allele depth (12,16) ok, GQ 99 ok, PL (477,0,367), PASS, seems to be
an accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
7. SYNE1 (idem Son): GCTTG heterozygous: potentially related to a carrier status
of autosomal recessive cerebellar ataxia type 1. Sequencing depth (49) ok,
allele depth (20,29), GQ 99 ok, PL (1498, 0,797), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
8. ABCA13 (only found in Father): CT heterozygous: This gene has not yet been
associated to a certain disease or trait, it functions as a transmembrane
transporter. Sequencing depth: 45 ok, allele depth (21,24) ok, GQ 99 ok, PL
(791,0,638), PASS, Polyphen 0,874, seems to be an accurate call, however
the variant itself remains of unknown clinical significance + unknown Sift
score.
9. HOGA1 (idem Son & Daughter): CT heterozygous: potentially related to a
carrier status of primary hyperoxaluria type 3, which can cause kidney damage.
sequencing depth (15) ok, allele depth (6,9) imbalance?, GQ 99 ok, PL
(277,0,189), PASS, seems to be an accurate call, however the variant itself
remains of unknown clinical significance + unknown Sift and polyphen
scores.
10. PNPLA2 (only found in Father): GT heterozygous: potentially related to a carrier
status of Neutral lipid storage disease with myopathy, a metabolic disease
characterised by muscle weakness, liver damage, heart problems and other
complications. Sequencing depth: 15 ok, allele depth (8,7) ok, GQ 99 ok, PL
(224,0,205), PASS, Polyphen 0,939, seems to be an accurate call, however
the variant itself remains of unknown clinical significance + unknown Sift
score.
11. SLCO1B3 (idem Son): TA heterozygous: this gene has been associated with
Rotor type hyperbilirubinemia, it functions as a transporter in the liver and plays
a role in bile acid and bilirubin transport. Sequencing depth (105) ok, allele
depth (58,47) ok, GQ 99 ok, PL (1494,0,1836), PASS, Polyphen score 1,
seems to be an accurate call, however the variant itself remains of
unknown clinical significance + unknown Sift score.
12. EIF2B2 (idem Son & Daughter): AG heterozygous: potentially related to a
carrier status of leukoencephalopathy with vanishing white matter, a
progressive neurological disorder. Sequencing depth (86) ok, allele depth
(42,44) ok, GQ 99 ok, PL (1484, 0, 1409), Polyphen score 0,948, PASS seems
to be an accurate call, however the variant itself remains of unknown
clinical significance + unknown Sift score.
13. PIF1 (idem Daughter): AC heterozygous: this gene has not yet been associated
with a certain disease or trait, it functions as a DNA helicase that negatively
regulates telomerase, a reverse transcriptase that maintains telomere length.
Sequencing depth (9) rather low, allele depth (5,4) ok, GQ 83 rather low, PL
(83,0,171), PASS, seems to be an accurate call, however the variant itself
20
remains of unknown clinical significance + unknown Sift and polyphen
scores and rather low sequencing depth and GQ.
14. HNF1B (idem Daughter): GT heterozygous: potentially pathogenic for MODY5
and/or renal cysts. Sequencing depth: 18 ok, allele depth (6;12) imbalance?,
GQ 99 ok, PL (396,0,167), PASS, Sift 0,05, seems to be an accurate call,
however the variant itself remains of unknown clinical significance +
unknown polyphen score.
15. DNM2 (idem Son): CT heterozygous: potentially pathogenic for centronuclear
myopathy, that affects skeletal muscles, or Charcot-Marie Tooth disease, a
neurological disorder with progressive muscle weakness. sequencing depth
(13) ok, allele depth (6,7) ok, GQ 99 ok, PL (196,0,147), PASS, seems to be
an accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
16. TMPRSS3 (only found in Father): AG heterozygous: potentially related to a
carrier status of non syndromic deafness type 8 autosomal recessive, or
Enteropeptidase deficiency, a metabolic disorder that causes severe diarrhea
and poor growth. Sequencing depth (33) ok, allele depth (18,15) ok, GQ 99 ok,
PL (489,0,612), PASS, seems to be an accurate call, however the variant
itself remains of unknown clinical significance + unknown Sift and
polyphen scores.
17. COL6A2 (idem Daughter & Son, daughter low GQ and depth): AAC
heterozygous: potentially pathogenic for Bethlem myopathy or related to a
carrier status of Ullrich congenital muscular dystrophy, sequencing depth: 15
ok, allele depth (6,9) ok, GQ 99 ok, PL (301,0,134), PASS, seems to be an
accurate call, however the variant itself remains of unknown clinical
significance + unknown Sift and polyphen scores.
18. XPNPEP3 (idem Son & Daughter): TTA heterozygous: potentially related to a
carrier status of nephronophthisis-like nephropathy, a kidney disease.
Sequencing depth (74) ok, allele depth (31,43), ok, GQ 99 ok, PL 1873,0,1150,
PASS, seems to be an accurate call, however the variant itself remains of
unknown clinical significance + unknown Sift and polyphen scores.
19. SHROOM4 (idem Daughter): TT homozygous (! gene is located on the Xchromosome, father is haploid and carries the Alt allele T): potentially related to
a carrier status of X-linked mental retardation. Sequencing depth (34) ok, allele
depth (0,34) ok, GQ 99 ok, PL (1323,102,0), PASS, seems to be an accurate
call, however the variant itself remains of unknown clinical significance +
unknown Sift and polyphen scores.
21
GeneTalk Report
Variant data of all exomes were also analyzed in GeneTalk with various filter settings
[1]. For Father this analysis yielded variants in 13 genes, among them CHI3L2, TPH1,
and FPR1. NM_004000: exon9: c.952C>T was reported to have a cis-regulatory effect
on the expression of CHI3L2, a gene that might be involved in cartilage biogenesis but
that has not been associated with any medical condition yet [2]. The heterozygous
variant NM_004179: exon7: c.898G>A: p.A300T reduces the activity of tryptophan
hydroxylase 1, TPH1, an enzyme that is required in the serotonin biosynthesis. Halmoy
et al. analysed off-springs of mothers with an impaired serotonin production and showed
that individuals score higher in average on an attention deficit/hyperactivity test [3]. In
the Corpas family this is allele would be straightforward for Father to consult, as only
female carriers would have the chance to affect their offspring. However, for Daughter
that turned out to have this allele transmitted by Father, the genetic consult would be
more challenging. In the community of geneticists there is growing support for
communicating variants that might be health related and actionable. The ACMG Board
published a list of actionable genes of which TPH1 is not part [4], and it is questionable
whether the medical advice to check serotonin levels especially during pregnancy would
be reasonable given the current data. The variant
NM_001193306:exon3:c.576T>G:p.N192K in FPR1 might be of relevance whenever a
carrier in the Corpas family requires some treatment with the immunosuppressant
ciclosporin [5]. The variants in the remaining genes were classified as likely nonpathogenic polymorphisms or artifacts by the GeneTalk expert community, although
they have been mentioned in the literature.
For Mother, filtering for heterozygous risk alleles yielded variants also in 13 genes. The
only variant that’s of potential interest in a clinical context is the missense mutation
R117W in P2RX7 that affects protein function and might play a role in affective mood
disorders [6]. However, in a genetic consultation about carrier risks, this allele would
probably not be communicated as it is without any practical implications.
We then analysed the exome quartet assuming the son of the Corpas family was
affected by some trait for which intended to find a genetic explanation. First, we filtered
for possibly pathogenic homozygous variants that might cause recessive diseases:
 Functional filter: missense, nonsense, splicing, frame shifting
 Frequency filter: minor allele frequency <0.1 %
 Inheritance filter: recessive, homozygous in affected individual only

We did not find any potentially pathogenic variants with these settings and adapted the
inheritance filter for recessive, compound heterozygous. This filtering approach is very
powerful for identifying pathogenic alleles in individuals from non-consanguineous
marriages that are affected by recessive disorders [7, 8] and yielded variants in
altogether nine genes, CELSR1, ZNF594, AHNAK2, ARHGEF17, MUC6, ZNF76,
MUC4, ALPPL2, and NBPF10. Most of these genes are known be highly variable or to
22
cause sequencing artefacts due to pseudogenes and would thus not been considered
as clinically relevant.
Finally we filtered for de novo mutations in Son, which is for instance a very promising
filtering approach when looking for pathogenic candidate mutations in patients with nonsyndromic intellectual disability [9]:
 Frequency Filter: remove all dbSNP entries
 Inheritance filter: set the status of the son to affected in the pedigree editor and
filter for dominant.
We identified one de novo mutation, NM_022911:exon6:c.609C>G:p.F203L in
SLC26A6 that codes for an anion exchanger that might limit the rate of intestinal oxalate
reabsorption [10]. The missense mutation is predicted to be pathogenic by
MutationTaster and if Son will ever experience a renal colic from kidney stones, this is
the genetics he might want to blame for it.
All analysis can also be reproduced in GeneTalk’s demo account with the quartet VCF
of the Corpas Family.
1. Kamphans T, Krawitz PM: GeneTalk: an expert exchange platform for assessing
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